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- PDB-5evc: Crystal structure of putative aspartate racemase from Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 5evc
TitleCrystal structure of putative aspartate racemase from Salmonella Typhimurium complexed with sulfate and potassium
ComponentsPutative aspartate racemase
KeywordsISOMERASE / racemase / alpha beta fold / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


amino-acid racemase activity / nitrogen compound metabolic process / metal ion binding
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold ...Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / FORMIC ACID / : / Aspartate racemase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaltseva, N. / Kim, Y. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To be published
Title: Crystal structure of putative aspartate racemase from Salmonella Typhimurium complexed with sulfate and potassium
Authors: Maltseva, N. / Kim, Y. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aspartate racemase
B: Putative aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,88213
Polymers58,2492
Non-polymers63311
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-65 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.328, 85.328, 113.997
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative aspartate racemase /


Mass: 29124.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM4510 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8ZJZ9

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Non-polymers , 7 types, 278 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium fluoride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→39.96 Å / Num. all: 50547 / Num. obs: 50547 / % possible obs: 97.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 12.79 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 27.65
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 3.428 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S7Z
Resolution: 1.7→39.957 Å / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.63 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1573 2568 5.08 %random
Rwork0.1352 ---
obs0.1368 50528 97.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→39.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 31 267 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053832
X-RAY DIFFRACTIONf_angle_d0.7815232
X-RAY DIFFRACTIONf_dihedral_angle_d16.5062338
X-RAY DIFFRACTIONf_chiral_restr0.053605
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73390.24081600.19252649X-RAY DIFFRACTION93
1.7339-1.76930.19281440.17372685X-RAY DIFFRACTION94
1.7693-1.80780.18861530.16172671X-RAY DIFFRACTION94
1.8078-1.84980.17771660.15142697X-RAY DIFFRACTION94
1.8498-1.89610.15091490.14482688X-RAY DIFFRACTION93
1.8961-1.94730.16131260.14162674X-RAY DIFFRACTION94
1.9473-2.00460.16791500.13722660X-RAY DIFFRACTION93
2.0046-2.06930.16671420.14332672X-RAY DIFFRACTION94
2.0693-2.14320.17051500.14182663X-RAY DIFFRACTION93
2.1432-2.22890.15231480.14332666X-RAY DIFFRACTION93
2.2289-2.33030.14971390.13352670X-RAY DIFFRACTION94
2.3303-2.45310.1451370.1322673X-RAY DIFFRACTION93
2.4531-2.60660.1561110.1412675X-RAY DIFFRACTION94
2.6066-2.80760.17831490.13982650X-RAY DIFFRACTION92
2.8076-3.08960.16771440.13992649X-RAY DIFFRACTION92
3.0896-3.53560.14951270.12452657X-RAY DIFFRACTION92
3.5356-4.45020.11711430.1112608X-RAY DIFFRACTION91
4.4502-24.63460.14891290.12232613X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5020.24920.4480.76120.03082.64190.00560.0050.03340.0177-0.07750.1683-0.0483-0.04650.03060.12060.0219-0.02850.0899-0.03610.0861-36.94834.2038-1.7899
22.44871.3738-0.83941.2371-1.15182.40030.09220.06850.0865-0.1004-0.03960.3015-0.0899-0.2425-0.03560.11170.0535-0.06460.1271-0.05380.1443-46.06955.0932-7.1555
31.2260.3157-0.03221.09580.24052.1203-0.04440.0830.0805-0.1087-0.01690.2262-0.2666-0.0540.07590.15890.0315-0.06470.1088-0.01910.0987-36.18916.6843-11.2517
46.9303-4.1301-0.79637.1291.1410.60120.15670.27780.0369-0.2767-0.08140.0552-0.269-0.0454-0.04380.23460.0074-0.04530.19170.01180.0784-28.60224.1973-16.3442
50.96290.1115-0.30122.37450.65452.4080.01390.1418-0.0563-0.20770.0209-0.17670.01760.5034-0.02580.1380.0285-0.02520.2598-0.03540.0678-20.2898.1018-15.9536
60.7210.87670.73691.9284-0.14752.0374-0.05570.02930.07030.040.0072-0.0155-0.06620.29080.07980.1162-0.0003-0.06180.1156-0.02720.0581-29.41413.90351.2946
74.04370.8195-5.2092.8106-0.03857.12990.024-0.3569-0.19130.0081-0.4112-0.09030.10960.41010.39680.41130.0156-0.11770.5850.0510.5587-38.295612.307618.2694
80.7830.0417-0.46960.87620.02590.662-0.05640.0678-0.07-0.1653-0.16120.42020.0627-0.31510.01470.1276-0.0031-0.05370.1546-0.09860.1975-44.8933-8.7087-2.832
90.6437-0.2174-0.11540.42130.14781.88980.00240.079-0.0208-0.0944-0.13260.08780.10940.04460.1150.15650.0231-0.01660.0958-0.02830.0702-31.7656-7.3024-5.3736
101.3235-0.58760.58760.8443-0.39342.9076-0.0138-0.0616-0.05430.0944-0.01320.29380.0645-0.22310.02170.1104-0.01720.04120.101-0.040.1223-43.0672-7.873611.8661
113.7206-1.27820.281.7614-0.19462.2516-0.05430.0508-0.24130.0009-0.06460.32890.1904-0.230.1190.1253-0.03250.03120.097-0.03010.1252-40.0216-18.41029.2916
120.9943-0.2642-0.63992.11961.60831.6137-0.1882-0.2415-0.13780.36040.14450.06670.45240.29660.02660.1990.06850.02110.15180.00910.074-25.2589-21.756515.0939
134.48262.27571.94845.77082.16272.03240.2328-0.5776-0.25020.7699-0.0322-0.1320.4605-0.2288-0.18510.28770.02240.00580.21330.050.1101-25.9537-26.297817
141.7442-0.45051.71742.2698-0.24354.1031-0.036-0.21340.08850.31210.0809-0.1121-0.13130.21130.16720.1494-0.03880.00080.2606-0.0830.0465-22.7683-5.248619.9875
151.55-0.13270.08813.37321.01271.68-0.0082-0.066-0.00930.1420.1031-0.350.02960.5178-0.06330.12820.02190.00290.2456-0.0310.0794-17.6632-11.984513.6245
161.3672-2.1651-0.15123.56830.65481.2638-0.01490.07390.2832-0.25580.0669-0.8036-0.06610.9572-0.11480.18180.00670.05910.4622-0.03040.2308-14.727-13.90086.043
170.6401-0.3798-0.77991.43150.32321.8801-0.10250.1715-0.1989-0.174-0.02490.24010.1698-0.18240.21930.1321-0.00110.00790.1169-0.06590.0905-35.4698-17.0373-4.6562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -3:60 )A-3 - 60
2X-RAY DIFFRACTION2( CHAIN A AND RESID 61:84 )A61 - 84
3X-RAY DIFFRACTION3( CHAIN A AND RESID 85:133 )A85 - 133
4X-RAY DIFFRACTION4( CHAIN A AND RESID 134:148 )A134 - 148
5X-RAY DIFFRACTION5( CHAIN A AND RESID 149:200 )A149 - 200
6X-RAY DIFFRACTION6( CHAIN A AND RESID 201:232 )A201 - 232
7X-RAY DIFFRACTION7( CHAIN A AND RESID 233:233 )A233
8X-RAY DIFFRACTION8( CHAIN B AND RESID -5:12 )B-5 - 12
9X-RAY DIFFRACTION9( CHAIN B AND RESID 13:41 )B13 - 41
10X-RAY DIFFRACTION10( CHAIN B AND RESID 42:84 )B42 - 84
11X-RAY DIFFRACTION11( CHAIN B AND RESID 85:111 )B85 - 111
12X-RAY DIFFRACTION12( CHAIN B AND RESID 112:133 )B112 - 133
13X-RAY DIFFRACTION13( CHAIN B AND RESID 134:148 )B134 - 148
14X-RAY DIFFRACTION14( CHAIN B AND RESID 149:166 )B149 - 166
15X-RAY DIFFRACTION15( CHAIN B AND RESID 167:200 )B167 - 200
16X-RAY DIFFRACTION16( CHAIN B AND RESID 201:213 )B201 - 213
17X-RAY DIFFRACTION17( CHAIN B AND RESID 214:232 )B214 - 232

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